Venkatesh Lab

Understanding Bacterial Metabolism

Our group is interested in evaluating the phenotypic characteristics of microbial systems by establishing the fluxes in metabolic networks. We employ flux balance methods and elementary mode analysis to determine the fluxes in the metabolic reaction network. The methodology can further be used to establish the effect of gene deletion and over-expression of enzymes on the fluxes, thereby linking the fluxes to the growth phenotype. These methods have been applied to growth of Escherichia coli, Corynebacterium glutamicum and Saccharomyces cerevisiae. Specifically, we have studied the effect of key transcriptional regulators on the growth of E. coli under different aeration conditions. The study focuses on the relevant question as to whether the global transcriptional regulators have a role in optimizing growth to achieve the three objectives of redox balance, energy generation and biomass synthesis. Further, to establish the connectivity between the genetic networks to the ensuing phenotype, we have developed a steady state modeling formalism for gene expression (SSGES) which includes molecular mechanisms that help in simulating microarray data with high accuracy and can be used to study the effect of both structural and parametric perturbation on gene expression. The expression of TF will then be further connected to the metabolic network.

E. coli metabolism

E. coli is a facultative anaerobic bacterium capable of surviving with (aerobic) or without (anaerobic) oxygen. We study the effect of key transcriptional regulators on the growth of E. coli under different aeration conditions. Transcriptional regulators or factors (TFs) play a key role in regulating the flux distribution in vivo. Many studies enumerate the role of important global transcription factors that regulate metabolism under various conditions.